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Merge pull request #635 from szilvajuhos/master
To process targeted sequencing with a target BED
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| #!/usr/bin/env bash | ||
| # this script concatenates all VCFs that are in the local directory: the | ||
| # purpose is to make a single VCF from all the VCFs that were created from different intervals | ||
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| usage() { echo "Usage: $0 [-i genome_index_file] [-o output.file.no.gz.extension] <-t target.bed> <-c cpus>" 1>&2; exit 1; } | ||
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| while getopts "i:c:o:t:" p; do | ||
| case "${p}" in | ||
| i) | ||
| genomeIndex=${OPTARG} | ||
| ;; | ||
| c) | ||
| cpus=${OPTARG} | ||
| ;; | ||
| o) | ||
| outputFile=${OPTARG} | ||
| ;; | ||
| t) | ||
| targetBED=${OPTARG} | ||
| ;; | ||
| *) | ||
| usage | ||
| ;; | ||
| esac | ||
| done | ||
| shift $((OPTIND-1)) | ||
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| if [ -z ${genomeIndex} ]; then echo "Missing index file "; usage; fi | ||
| if [ -z ${cpus} ]; then echo "No CPUs defined: setting to 1"; cpus=1; fi | ||
| if [ -z ${outputFile} ]; then echo "Missing output file name"; usage; fi | ||
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| set -euo pipefail | ||
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| # first make a header from one of the VCF intervals | ||
| # get rid of interval information only from the GATK command-line, but leave the rest | ||
| FIRSTVCF=$(ls *.vcf | head -n 1) | ||
| sed -n '/^[^#]/q;p' $FIRSTVCF | \ | ||
| awk '!/GATKCommandLine/{print}/GATKCommandLine/{for(i=1;i<=NF;i++){if($i!~/intervals=/ && $i !~ /out=/){printf("%s ",$i)}}printf("\n")}' \ | ||
| > header | ||
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| # Get list of contigs from the FASTA index (.fai). We cannot use the ##contig | ||
| # header in the VCF as it is optional (FreeBayes does not save it, for example) | ||
| CONTIGS=($(cut -f1 ${genomeIndex})) | ||
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| # concatenate VCFs in the correct order | ||
| ( | ||
| cat header | ||
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| for chr in "${CONTIGS[@]}"; do | ||
| # Skip if globbing would not match any file to avoid errors such as | ||
| # "ls: cannot access chr3_*.vcf: No such file or directory" when chr3 | ||
| # was not processed. | ||
| pattern="${chr}_*.vcf" | ||
| if ! compgen -G "${pattern}" > /dev/null; then continue; fi | ||
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| # ls -v sorts by numeric value ("version"), which means that chr1_100_ | ||
| # is sorted *after* chr1_99_. | ||
| for vcf in $(ls -v ${pattern}); do | ||
| # Determine length of header. | ||
| # The 'q' command makes sed exit when it sees the first non-header | ||
| # line, which avoids reading in the entire file. | ||
| L=$(sed -n '/^[^#]/q;p' ${vcf} | wc -l) | ||
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| # Then print all non-header lines. Since tail is very fast (nearly as | ||
| # fast as cat), this is way more efficient than using a single sed, | ||
| # awk or grep command. | ||
| tail -n +$((L+1)) ${vcf} | ||
| done | ||
| done | ||
| ) | bgzip -@${cpus} > rawcalls.vcf.gz | ||
| tabix rawcalls.vcf.gz | ||
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| set +u | ||
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| # now we have the concatenated VCF file, check for WES/panel targets, and generate a subset if there is a BED provided | ||
| echo "target is $targetBED" | ||
| if [ ! -z ${targetBED+x} ]; then | ||
| echo "Selecting subset..." | ||
| bcftools isec --targets-file ${targetBED} rawcalls.vcf.gz | bgzip -@${cpus} > ${outputFile}.gz | ||
| tabix ${outputFile}.gz | ||
| else | ||
| # simply rename the raw calls as WGS results | ||
| for f in rawcalls*; do mv -v $f ${outputFile}${f#rawcalls.vcf}; done | ||
| fi | ||
|
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